AB0626 DIFFERENTIALLY EXPRESSED GENES (DEGS) OVERLAP AMONG BLOOD SAMPLES DATASETS FROM PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) THROUGH INTEGRATIVE BIOINFORMATICS METANALYSIS
Authors: R. Martinez, A. Gonzáles Godínez, I. Vasquez Tercero, C. Elizondo Solis, A. Montoya Rosales, M. Salinas Carmona, N. Macias-Segura
Journal: Annals of the Rheumatic Diseases (2023)

<h3>Background</h3> Systemic Lupus Erythematosus is an autoimmune chronic disease mainly characterized by the presence of auto-autoantibodies, and periods of flares and remission [1]. Understanding the mechanisms of physiopathology is still being the aim for several researchers. In the last 20 years multiple studies tried to look for molecular mechanisms associated to the disease using biomolecular techniques [2]. Specifically, the gene expression patterns play an important role in the pathophysiology of this disease, in which the interferon signature has been widely found in SLE patients, but also in other autoimmune diseases like rheumatoid arthritis and Sjögren's syndrome [3]. However, there is a discordance in which genes from the interferon signature are specific biomarkers for SLE, since there are multiple studies that describe the interferon signature but with different differentially expressed genes. <h3>Objectives</h3> We aimed to identify differentially expressed genes that overlap across different datasets of gene expression from blood samples of SLE patients using an integrative bioinformatics metanalysis. <h3>Methods</h3> We design a search strategy in the Gene Expression Omnibus platform to identify data sets of gene expression profile by array from blood samples of patients with SLA. The inclusion criteria were: 1) assays performed in humans, 2) the dataset include SLE patients and healthy controls, 3) expression profiling by array, 4) data analysis using GEO2R, 5) samples from blood. The exclusion criteria was: 1) incomplete information of the genes, 2) gene expression by RNAseq. Differentially expressed genes were selected when logfold change was &gt;2 with <i>p</i> &lt;0.05. Integrative bioinformatics strategy was applied. Using the platforms GeneMania and DAVID we identify overlapped genes among datasets and functional enrichment analysis of the differentially expressed genes. <h3>Results</h3> We selected 3 datasets that fulfill the inclusion criteria: GSE110174, GSE10325, and GSE154851. A total of 29 up-regulated genes were identified among datasets. Venn diagram shows 3 genes overlapped among all the datasets, and 1 or 2 genes overlapped between different pairs of datasets (Figure 1). A prediction analysis yielded 20 co-expressed genes, that interact with the overlapped genes. A functional enrichment analysis yielded the 3 principal biological processes involving those genes: 17 genes participate in defense response to virus; 13 genes associated to response to virus; and 8 genes involved in negative regulation of viral genome replication (Table 1). Most of the genes identified belong to the interferon signature. <h3>Conclusion</h3> We aimed to obtain upregulated genes and their co-expressed pairs through transcriptomic and functional enrichment analysis. 6 genes appeared upregulated across the 3 datasets, and 20 genes were listed as their co-expressed pairs. Those genes were involved in the processes of Defense Response to Virus, Response to virus, and Negative Regulation of Viral Genome Replication. These genes can serve as possible biomarkers for early diagnosis, and maybe even possible therapeutic targets. <h3>References</h3> [1]Yu, C., M.E. Gershwin, and C. Chang, <i>Diagnostic criteria for systemic lupus erythematosus: a critical review.</i> Journal of autoimmunity, 2014. <b>48</b>: p. 10-13. [2]Fujio, K., et al., <i>transcriptome and trans-omics analysis of systemic lupus erythematosus.</i> Inflammation and regeneration, 2020. <b>40</b>(1): p. 1-6. [3]Rönnblom, L. and M.-L. Eloranta, <i>The interferon signature in autoimmune diseases.</i> Current opinion in rheumatology, 2013. <b>25</b>(2): p. 248-253. <h3>Acknowledgements:</h3> NIL. <h3>Disclosure of Interests</h3> None Declared.